Alter

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DESCRIPTION

"alter" changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in the name space are:

  name, resn, resi, chain, alt, elem, q, b, segi,
  type (ATOM,HETATM), partial_charge, formal_charge,
  text_type, numeric_type, ID

All strings must be explicitly quoted. This operation typically takes several seconds per thousand atoms altered.

WARNING: You should always issue a "sort" command on an object after modifying any property which might affect canonical atom ordering (names, chains, etc.). Failure to do so will confound subsequent "create" and "byres" operations.

USAGE

alter (selection),expression

EXAMPLES

  alter (chain A),chain='B'
  alter (all),resi=str(int(resi)+100)
  sort

SEE ALSO

  Cmd alter_state, Cmd iterate, Cmd iterate_state, Cmd sort